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Long non-coding RNAs contribute to dosage compensation in both mammals and  Drosophila  by inducing changes in the chromatin structure of the X-chromosome. In  Drosophila melanogaster ,  roX1  and  roX2  are long non-coding RNAs that together with proteins form the male-specific lethal (MSL) complex, which coats the entire male X-chromosome and mediates dosage compensation by increasing its transcriptional output. Studies on polytene chromosomes have demonstrated that when both  roX1  and  roX2  are absent, the MSL-complex becomes less abundant on the male X-chromosome and is relocated to the chromocenter and the 4 th  chromosome. Here we address the role of  roX  RNAs in MSL-complex targeting and the evolution of dosage compensation in  Drosophila . We performed ChIP-seq experiments which showed that MSL-complex recruitment to high affinity sites (HAS) on the X-chromosome is independent of  roX  and that the HAS sequence motif is conserved in  D. simulans . Additionally, a complete and enzymatically active MSL-complex is recruited to six specific genes on the 4 th  chromosome. Interestingly, our sequence analysis showed that in the absence of  roX  RNAs, the MSL-complex has an affinity for regions enriched in  Hoppel  transposable elements and repeats in general. We hypothesize that  roX  mutants reveal the ancient targeting of the MSL-complex and propose that the role of  roX  RNAs is to prevent the binding of the MSL-complex to heterochromatin.

Non-coding roX RNAs Prevent the Binding of the MSL-complex to Heterochromatic Regions